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Gene: RARB |
Gene summary for RARB |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RARB | Gene ID | 5915 |
| Gene name | retinoic acid receptor beta | |
| Gene Alias | HAP | |
| Cytomap | 3p24.2 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | F1D8S6 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 5915 | RARB | CCI_3 | Human | Cervix | CC | 1.80e-21 | 1.15e+00 | 0.516 |
| 5915 | RARB | AEH-subject3 | Human | Endometrium | AEH | 2.33e-18 | 5.01e-01 | -0.2576 |
| 5915 | RARB | AEH-subject4 | Human | Endometrium | AEH | 1.60e-14 | 5.55e-01 | -0.2657 |
| 5915 | RARB | AEH-subject5 | Human | Endometrium | AEH | 1.92e-17 | 5.17e-01 | -0.2953 |
| 5915 | RARB | EEC-subject1 | Human | Endometrium | EEC | 3.48e-03 | 2.27e-01 | -0.2682 |
| 5915 | RARB | EEC-subject2 | Human | Endometrium | EEC | 1.05e-07 | 2.60e-01 | -0.2607 |
| 5915 | RARB | EEC-subject4 | Human | Endometrium | EEC | 1.17e-03 | 2.43e-01 | -0.2571 |
| 5915 | RARB | EEC-subject5 | Human | Endometrium | EEC | 4.37e-04 | 2.21e-01 | -0.249 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:00305229 | Cervix | CC | intracellular receptor signaling pathway | 60/2311 | 265/18723 | 1.89e-06 | 5.97e-05 | 60 |
| GO:00605375 | Cervix | CC | muscle tissue development | 76/2311 | 403/18723 | 9.76e-05 | 1.27e-03 | 76 |
| GO:00147064 | Cervix | CC | striated muscle tissue development | 72/2311 | 384/18723 | 1.76e-04 | 2.07e-03 | 72 |
| GO:000206410 | Cervix | CC | epithelial cell development | 45/2311 | 220/18723 | 4.14e-04 | 4.21e-03 | 45 |
| GO:00426924 | Cervix | CC | muscle cell differentiation | 69/2311 | 384/18723 | 8.12e-04 | 7.09e-03 | 69 |
| GO:00519603 | Cervix | CC | regulation of nervous system development | 77/2311 | 443/18723 | 1.13e-03 | 9.30e-03 | 77 |
| GO:00487365 | Cervix | CC | appendage development | 35/2311 | 172/18723 | 1.88e-03 | 1.39e-02 | 35 |
| GO:00601735 | Cervix | CC | limb development | 35/2311 | 172/18723 | 1.88e-03 | 1.39e-02 | 35 |
| GO:00511464 | Cervix | CC | striated muscle cell differentiation | 50/2311 | 283/18723 | 5.53e-03 | 3.19e-02 | 50 |
| GO:00309003 | Cervix | CC | forebrain development | 64/2311 | 379/18723 | 5.53e-03 | 3.19e-02 | 64 |
| GO:0150063 | Cervix | CC | visual system development | 63/2311 | 375/18723 | 6.58e-03 | 3.65e-02 | 63 |
| GO:0001654 | Cervix | CC | eye development | 62/2311 | 371/18723 | 7.83e-03 | 4.13e-02 | 62 |
| GO:0048880 | Cervix | CC | sensory system development | 63/2311 | 381/18723 | 9.29e-03 | 4.66e-02 | 63 |
| GO:0061351 | Cervix | CC | neural precursor cell proliferation | 28/2311 | 145/18723 | 1.04e-02 | 4.97e-02 | 28 |
| GO:00605376 | Endometrium | AEH | muscle tissue development | 83/2100 | 403/18723 | 2.57e-08 | 1.50e-06 | 83 |
| GO:003052210 | Endometrium | AEH | intracellular receptor signaling pathway | 60/2100 | 265/18723 | 7.16e-08 | 3.77e-06 | 60 |
| GO:00147065 | Endometrium | AEH | striated muscle tissue development | 75/2100 | 384/18723 | 1.06e-06 | 3.62e-05 | 75 |
| GO:00016556 | Endometrium | AEH | urogenital system development | 67/2100 | 338/18723 | 2.30e-06 | 6.76e-05 | 67 |
| GO:00720015 | Endometrium | AEH | renal system development | 61/2100 | 302/18723 | 3.43e-06 | 9.24e-05 | 61 |
| GO:00018224 | Endometrium | AEH | kidney development | 57/2100 | 293/18723 | 2.25e-05 | 4.35e-04 | 57 |
| Page: 1 2 3 4 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa052226 | Cervix | CC | Small cell lung cancer | 29/1267 | 92/8465 | 4.38e-05 | 3.09e-04 | 1.83e-04 | 29 |
| hsa052234 | Cervix | CC | Non-small cell lung cancer | 21/1267 | 72/8465 | 1.48e-03 | 6.32e-03 | 3.74e-03 | 21 |
| hsa0522213 | Cervix | CC | Small cell lung cancer | 29/1267 | 92/8465 | 4.38e-05 | 3.09e-04 | 1.83e-04 | 29 |
| hsa0522313 | Cervix | CC | Non-small cell lung cancer | 21/1267 | 72/8465 | 1.48e-03 | 6.32e-03 | 3.74e-03 | 21 |
| Page: 1 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| RARB | CHO | Liver | Cirrhotic | EDEM1,PRICKLE1,CREB5, etc. | 3.73e-01 |  |
| RARB | CHO | Liver | NAFLD | EDEM1,PRICKLE1,CREB5, etc. | 4.95e-01 |  |
| RARB | GMC | Stomach | CSG | KCNC4,LINC00342,EHHADH, etc. | 1.41e-01 |  |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| RARB | SNV | Missense_Mutation | c.184N>C | p.Glu62Gln | p.E62Q | P10826 | protein_coding | deleterious(0.05) | possibly_damaging(0.864) | TCGA-A2-A0SY-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | arimidex | SD | |
| RARB | SNV | Missense_Mutation | c.205N>T | p.Pro69Ser | p.P69S | P10826 | protein_coding | deleterious(0.02) | possibly_damaging(0.839) | TCGA-AN-A041-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RARB | SNV | Missense_Mutation | c.505N>C | p.Glu169Gln | p.E169Q | P10826 | protein_coding | tolerated(0.06) | benign(0.213) | TCGA-AN-A049-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RARB | SNV | Missense_Mutation | c.434G>A | p.Gly145Glu | p.G145E | P10826 | protein_coding | deleterious(0) | possibly_damaging(0.903) | TCGA-B6-A0IN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| RARB | SNV | Missense_Mutation | c.206N>T | p.Pro69Leu | p.P69L | P10826 | protein_coding | deleterious(0.02) | possibly_damaging(0.887) | TCGA-C8-A132-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RARB | SNV | Missense_Mutation | c.860N>A | p.Arg287Gln | p.R287Q | P10826 | protein_coding | deleterious(0.02) | possibly_damaging(0.812) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| RARB | SNV | Missense_Mutation | c.1173N>C | p.Leu391Phe | p.L391F | P10826 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-C5-A1BK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| RARB | SNV | Missense_Mutation | c.440N>T | p.Ser147Phe | p.S147F | P10826 | protein_coding | deleterious(0) | probably_damaging(0.968) | TCGA-C5-A7CL-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | PD | |
| RARB | SNV | Missense_Mutation | c.1058N>C | p.Lys353Thr | p.K353T | P10826 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| RARB | SNV | Missense_Mutation | c.339G>C | p.Met113Ile | p.M113I | P10826 | protein_coding | deleterious(0) | possibly_damaging(0.794) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| 5915 | RARB | NUCLEAR HORMONE RECEPTOR, DRUGGABLE GENOME | agonist | 135651435 | TRETINOIN | |
| 5915 | RARB | NUCLEAR HORMONE RECEPTOR, DRUGGABLE GENOME | R667 | |||
| 5915 | RARB | NUCLEAR HORMONE RECEPTOR, DRUGGABLE GENOME | agonist | CHEMBL38 | TRETINOIN | |
| 5915 | RARB | NUCLEAR HORMONE RECEPTOR, DRUGGABLE GENOME | ALITRETINOIN | ALITRETINOIN |
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